bioguider 0.2.31__tar.gz → 0.2.33__tar.gz

{bioguider-0.2.31 → bioguider-0.2.33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.31
+Version: 0.2.33
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.31 → bioguider-0.2.33}/bioguider/agents/agent_utils.py

@@ -27,6 +27,7 @@ from bioguider.utils.utils import clean_action_input
 from ..utils.gitignore_checker import GitignoreChecker
 from ..database.summarized_file_db import SummarizedFilesDb
 from bioguider.agents.common_conversation import CommonConversation
+from bioguider.rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -66,8 +67,17 @@ def get_llm(
     api_version: str=None,
     azure_deployment: str=None,
     temperature: float = 0.0,
-    max_tokens: int = 4096,
+    max_tokens: int = 16384,  # Set high by default - enough for any document type
 ):
+    """
+    Create an LLM instance with appropriate parameters based on model type and API version.
+    
+    Handles parameter compatibility across different models and API versions:
+    - DeepSeek models: Use max_tokens parameter
+    - GPT models (newer): Use max_completion_tokens parameter
+    - GPT-5+: Don't support custom temperature (uses default)
+    """
+    
     if model_name.startswith("deepseek"):
         chat = ChatDeepSeek(
             api_key=api_key,
@@ -76,23 +86,38 @@ def get_llm(
             max_tokens=max_tokens,
         )
     elif model_name.startswith("gpt"):
-        chat = AzureChatOpenAI(
-            api_key=api_key,
-            azure_endpoint=azure_endpoint,
-            api_version=api_version,
-            azure_deployment=azure_deployment,
-            model=model_name,
-            temperature=temperature,
-            max_tokens=max_tokens,
-        )
+        # Base parameters common to all GPT models
+        llm_params = {
+            "api_key": api_key,
+            "azure_endpoint": azure_endpoint,
+            "api_version": api_version,
+            "azure_deployment": azure_deployment,
+            "model": model_name,
+        }
+        
+        # Determine token limit parameter name based on API version
+        # Newer APIs (2024-08+) use max_completion_tokens instead of max_tokens
+        use_completion_tokens = api_version and api_version >= "2024-08-01-preview"
+        token_param = "max_completion_tokens" if use_completion_tokens else "max_tokens"
+        llm_params[token_param] = max_tokens
+        
+        # Handle temperature parameter based on model capabilities
+        # GPT-5+ models don't support custom temperature values
+        supports_temperature = not any(restricted in model_name for restricted in ["gpt-5", "o1", "o3"])
+        if supports_temperature:
+            llm_params["temperature"] = temperature
+            
+        chat = AzureChatOpenAI(**llm_params)
     else:
-        raise ValueError("Invalid model name")
-    # validate chat
+        raise ValueError(f"Unsupported model type: {model_name}")
+    
+    # Validate the LLM instance with a simple test
     try:
         chat.invoke("Hi")
     except Exception as e:
-        print(e)
+        logger.error(f"Failed to initialize LLM {model_name}: {e}")
         return None
+    
     return chat
 
 def pretty_print(message, printout = True):
@@ -153,7 +178,9 @@ def read_directory(
         return None
     gitignore_checker = GitignoreChecker(
         directory=dir_path,
-        gitignore_path=gitignore_path
+        gitignore_path=gitignore_path,
+        exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+        exclude_file_patterns=configs["file_filters"]["excluded_files"],
     )
     files = gitignore_checker.check_files_and_folders(level=level)
     return files

{bioguider-0.2.31 → bioguider-0.2.33}/bioguider/agents/evaluation_readme_task.py

@@ -28,6 +28,7 @@ from bioguider.utils.constants import (
     EvaluationREADMEResult,
 )
 from bioguider.utils.utils import increase_token_usage
+from bioguider.rag.config import configs
 
 logger = logging.getLogger(__name__)
 
@@ -638,7 +639,9 @@ class EvaluationREADMETask(EvaluationTask):
         repo_path = self.repo_path
         gitignore_path = Path(repo_path, ".gitignore")
         gitignore_checker = GitignoreChecker(
-            directory=repo_path, gitignore_path=gitignore_path
+            directory=repo_path, gitignore_path=gitignore_path,
+            exclude_dir_patterns=configs["file_filters"]["excluded_dirs"],
+            exclude_file_patterns=configs["file_filters"]["excluded_files"],
         )
         found_readme_files = gitignore_checker.check_files_and_folders(
             check_file_cb=lambda root_dir, relative_path: Path(relative_path).name.lower() in possible_readme_files,